The recent development in genome engineering, for instance exemplified by Multiplex Automated Genomic Engineering (MAGE) and applications of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated protein 9 (Cas9) or other types of genome editing facilitated by engineered nucleases, such as Zinc finger nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs), in combination with decreased costs for DNA oligonucleotide synthesis, makes it possible to generate large cell libraries with overwhelming genetic diversity. At the same time technology development has led to the possibility of determining phenotypic and genotypic characteristics of cells. For instance, Fluidigm Dynamic Array™ integrated fluidic circuits (IFC) can be used for genotyping in a single microwell plate. However, the size of the cell libraries that can be analyzed is restricted to a few hundred different cells since the genetically different cells must be kept sorted and analyzed individually.
Another technology that can handle significantly larger strain libraries than Fluidigm Dynamic Array™ IFC is fluorescence-activated cell sorting (FACS). However, FACS has limitations since the phenotypic characterization of the cell libraries is limited to fluorescence readout at a single point in time. In vitro compartmentalization (IVC) and droplet-based technology can, similar to FACS, handle large libraries. However, the phenotypic information obtained in IVC is limited because of optical constraints for imaging in droplets and by the fact that long term cell growth experiments cannot be performed in the droplets.
Yet other techniques depend on adding barcoded oligomers to cells after imaging. The need for distribution of oligomers to specific spatial positions limits the conditions under which cells can be grown and the number of different barcodes that can be distributed.
Thus, there is a need for improvements within the technical field of phenotypic and genotypic characterization of cell libraries. In particular, there is a need for a technology that can handle large cell libraries and that can monitor phenotypic characteristics with high spatial and temporal resolution.